


Why We Run

by TARDISTraveller42



Category: Doctor Who, Doctor Who (2005)
Genre: Angst, Feels, Gen, Hurt/Comfort, Oneshot, Series 10, St. Luke's University, TARDIS - Freeform, The vault, Whump, the Master - Freeform
Language: English
Status: Completed
Published: 2017-12-18
Updated: 2017-12-18
Packaged: 2019-02-16 19:21:32
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 4,005
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/13060503
Author URL: https://archiveofourown.org/users/TARDISTraveller42/pseuds/TARDISTraveller42
Summary: After years in the Vault and St. Luke's Univeristy, Missy and the Doctor are both facing moral crises. One of those moral crises turns deadly.





	Why We Run

**Author's Note:**

> Be warned this is very, VERY angsty and there is a bit of Doctor whump as well. There is nothing graphic or gory, but there is also something of a mental breakdown. Take care, but please enjoy!

The Doctor sat marking Bill’s latest essay -- The Physics of the Moon -- pretending not to notice the young woman staring at him from across the desk. 

Bill sat watching the Doctor write with about a thousand things on her mind, but only one question. 

“Doctor,” she started. He looked up with those wide, owlish eyes, as if he hadn’t noticed her there before. “Why are you always running?”

He turned back to her essay and she had to suppress a sigh. Nardole had said it best. Every time the conversation turned serious…

“I don’t always run.” 

He stated it so simply and outright that Bill couldn’t help the disbelieving chuckle that escaped. He looked back up at her and she silenced herself. Something about his eyes made him ageless. In that moment, he could have been twenty or two thousand. 

The Doctor set his pen down and folded his hands together. “Sometimes I stay. Like I’m doing here.”

“Except for our trips in the TARDIS.”

They shared a playful grin. “Alright,” he conceded. “Apart from that.”

Bill wasn’t satisfied. “You still haven’t answered my question.”

His eyes looked away again, back to the essay, much more distant than before. “Bill, I think you know why.”

Bill waited for further explanation, but it never came. Instead, the Doctor cleared his throat, sat back, and passed her the essay. “Nice work. You know we should celebrate. There are these people who colonize the moon in the twenty-third century, ‘Mooninites’. I think you’d like them.”

“Mooninites?”

The Doctor gave her a quick smirk and went to the TARDIS. He leaned on her old wood finish and looked up at the windows. “Friendly people; music lovers. Just watch out for their teeth. They can get a bit bitey if you're not careful.”

Bill let herself forget about their conversation...for now. She stuffed her essay into her bag and hurried into the TARDIS without hesitation. The box disappeared from the room a few seconds later.

….

The Doctor entered the Vault late that night, a Mooninites song stuck in his head and an unopened bottle of wine in his hand. A few small scratches marred the skin under his left ear.

“Mooninites really have all of the fun.”

The Doctor dropped into the chair in front of Missy’s platform, letting the bottle almost hit the floor. Missy didn’t respond, her eyes focused on the wall. The Doctor leaned forward and noticed there were tears hidden in them. 

“Missy?”

She wiped her eyes with one aggressive hand. Her chest rose and fell shakily. “I’m remembering more and more now. All of the people I killed. The civilizations I destroyed.”

The Doctor leaned forward, placing the bottle on the floor with the care of someone in the presence of a bear. “Good.”

Her face turned toward his with a jolt. One tear slowly tracked down her cheek. “Good?” Her accent mixed with the tightness in her throat made it sound like so much more than a four letter primary school word. “You think it’s good?”

“Yes.”

She jumped to her feet. The Doctor didn’t let a flash of fear cross his face, though his hearts did skip a beat or two for a moment. She simply stared at him, clenching and unclenching her fists. Finally, she broke his gaze and pivoted to the platform behind.

The Doctor stood slowly. “It’s Hell. I know; trust me. I’ve been there.”

She clicked her teeth at him, and turned her face just enough to see him in the corner of her eye. “Darling, no offence, but you have no idea what Hell is like. How many have you killed? How many lives have you ruined?”

The Doctor steeled himself. “Too many to count.”

“But always for a good cause.”

Missy turned fully, and took a step forward. “You destroyed Gallifrey, but in a different universe, and for the safety of the world. You’ve led people to their deaths, but only because you wanted to show them how wonderful they were. You have killed some, but only the ruthless and the cruel and the unforgivable.”

She took another few steps toward him. Now her eyes were shining brightly. “You won’t even kill me because you’re so good.”

The Doctor looked away from her, focusing on the platform and the wall and anything but those eyes. Those eyes he’d known all his lives.

“Missy, I have done bad things for bad reasons. I have walked on battlefields I created.”

“But you still don’t understand!”

Missy grabbed the bottle off of the floor and held it pointedly at the Doctor. “I’ve killed innocent people for the fun of it. I set houses on fire just to watch them burn. I wasn’t doing it out of mercy or kindness or even anger. It’s my weekend out! It’s my playtime! It’s how I have fun!”

She threw the bottle at the wall, the glass shattering. The Doctor couldn’t help but flinch and cover his eyes as a few shards landed just a few feet away. He glance over to survey the damage, but instantly felt his wrist go into a death grip in Missy’s hand.

“Look at me!”

He did look at her. And even then, with her unwinding at the seams, he could only see his friend. He still could only forgive.

“Missy, you will get through this. I’m going to help you-”

“What if I don’t want to be helped anymore, Doctor?” Missy reached into a pocket in her skirt and pulled out something the Doctor recognized with a racing pulse. “What if I still want to be bad?”

The Doctor eyed the device in her hands. If he wasn’t mistaken, it was the third edition of the Thals’ motive laser gun, one of the shoddier prototypes of a Dalek gun.

“Missy,” he said, licking his lips and holding up his hands. “I can help you. I know it’s confusing.”

“Except it’s not, really, is it? You’re life is like a kiddie show. You show up, all heroic, and you beat the bad guys. Then more bad guys come, and you beat them too. Even me. Every time. It’s like clockwork for you. You don’t even have to wonder how it’ll end anymore.”

The Doctor stood his ground, even as she waved the weapon around like a toy. He couldn’t give up on her. Not now. Not after everything. “I don’t always win, Missy. I lose. All the time, I lose.”

Missy shook her head. “And then you run. I know. It’s always one of those two: you win, or you run. You beat the bad guys, or you run from them. What’ll it be today, Doctor? I’m still a baddie, aren’t I?”

The Doctor hardly dared to blink, trying to read into her. Was this a test? Or was she just truly in need of help? If that was the case, could he help her? Was he in over his head?

He cleared his throat. “There’s a third option.”

“Oh?”

His brain flitted around, trying to form words that made sense. Words that were honest.

“Yes. I’m still trying to learn how to do it.” He lowered his hands, fighting every natural response in his body. “Forgiveness.”

Her hand trembled at the word, and then raised the weapon to meet his chest. “Forgiveness?”

He nodded, keeping his eyes locked on hers. “Yes.”

She let out a laugh. “You probably have some plan, don’t you? You always have a plan. Is Noddy hanging around somewhere waiting on your signal?”

“No.”

“What about the questions girl? I guess she’s going to come up behind me with your silly screwdriver, right?”

“No.”

Missy’s lips curled into a sneer. “Then you’ll run. Like I always knew you would. You’ll run and I’ll burn down this university and nothing will have changed between us. Maybe you’ll sulk for a few years, and then you’ll find a new girl to kidnap.”

The Doctor felt his resolve bending, but he straightened himself and took a deep breath. “No, Missy. Not this time. This time I’m going to stay.”

Missy’s sneer turned into a frown. Then the tears came rolling down her face again. “Run away, Doctor. Run and never look back. Run!”

The Doctor stayed as still as he could. He couldn’t feel his legs enough to move them anyway. His hearts wouldn’t carry him, either. They were pumping too quickly and breaking all at once. He felt a tear blink into his eye.

“Missy, I’m not going anywhere.”

“You always RUN!”

The weapon went off.

A blue flash of light came speeding out of its tip, lighting the Doctor’s watery eyes with its brilliant glow. He watched it approach him as he stood stuck still to the spot. 

And then he saw it go through him, right between his two hearts. His scream melted in with Missy’s as he dropped to the floor of the Vault, chest burning and sense of the world around him fading.

The weapon dripped out of Missy’s limp hand as she dashed forward to catch the Doctor’s skull before it reached the concrete. Her knees collided with the ground as she took him into her arms, cradling his head in one hand and holding his middle on her lap with the other. 

“Why didn’t you run? You should have run!”

The Doctor gazed up at Missy, the world shifting and turning nauseously. He felt the hands holding him trembling. His finger brushed against her cotton skirt and he gripped it weakly, a tiny piece of reality to hold onto. His own legs and arms were starting to go numb.

“I won’t...give up on you, Missy. Never.” His eyes shut tightly as a wave of pain fluttered through his chest. “Never.”

Missy’s tears dropped to his cheek and lips. “I’m sorry. I’m sorry. For everything. Everything.”

Missy touched her forehead to the Doctor’s. Instantly there was a connection, tapping into their old, old psychic abilities. Every word from the Doctor’s end formed into ‘you are forgiven’. Missy let out a sob.

The door to the Vault burst open, and Missy’s eyes flew up. 

It was Nardole. 

He was cross. Oh, he was cross. But he was quiet about that. His mouth fell open at first, stunned into silence, and then he seemed to transform. Without another moment’s hesitation, he knelt beside the Doctor, who Missy placed on the ground, and steeled his voice.

“What happened?”

Missy wiped at her eyes, sniffing. Nardole touched two fingers to the Doctor’s neck. He looked up at her and snapped, “What happened?”

He leaned down and listened to the Doctor’s fast breathing for a moment as Missy gained slight composure.

“It was me. I...I-”

“What was he injured with?”

Missy handed over the weapon, holding it a foot away from her between two fingers, with the face of one holding a cockroach. Nardole examined it for a second, and then tossed it aside. 

“Where was he hit?”

Missy pointed to a general area on the Doctor’s chest. Nardole swiftly set about undoing his top few buttons. When he pulled the white cloth aside, he found an angry red mark two inches wide. The Doctor’s head lolled back and forth as he groaned.

“Get the TARDIS. Bill should be in the office. Bring her, too.” He looked up at Missy, who was still staring blankly at the Doctor’s injury. “Now!”

Missy jumped up and sprinted out of the Vault at top speed. Nardole turned back to the Doctor, eyes softening.

“Doctor? Doctor, can you hear me?”

Nardole put a gentle hand on the Doctor’s cheek. Blue eyes cracked open in response. Nardole smiled. “There you go. There you are. You’re gonna be fine, alright?”

The Doctor breathed rapidly through his nose, eyes widening. The world was blurring in and out, Nardole’s voice distant.

“Doctor? Stay with me, please.” With chattering teeth, Nardole looked up at the empty space in front of them. “The TARDIS should be here soon,” he stated with more assurance than he truly possessed. “You just stay with me.”

The Doctor’s head rolled toward him, eyelids fluttering. “Nardole.”

His voice was raspy, and it sent chills down Nardole’s spine. He took the Doctor’s hand in his own and rubbed the back of it.

“You fixed me, now I’m going to fix you, alright?”

The Doctor tightened his hold on Nardole’s hand. Nardole looked up at the ceiling. “Where the hell is she?”

“Nardole, please,” the Doctor paused, breathing deeply. “Don’t be cross with her.”

Nardole shook his head. “How can I not be? Look at what she did!”

The Doctor fixed Nardole with the strongest stare he could muster. “Please, promise me.”

Nardole rubbed the top of the Doctor’s hand. “Alright, alright. We’re forgiving her. But you have to stay awake. You can’t go leaving us with her, alright? Oi! Look at me when I’m talking, eh?”

A ghost of a smile crossed the Doctor’s lips as his heavy lids opened again. There was pain in his eyes; more pain than Nardole had seen in them for a long, long time. He bit his lip and wished and prayed.

A noise entered the space. 

The familiar, wonderful groan of the TARDIS. Then a second later, a pair of trainers clattering against the floor, bounding toward them.

“Doctor!”

Bill dropped to her knees opposite Nardole, horrified eyes looking over her tutor and best friend with suppressed tears.

“Oh my God. Is he gonna be alright?”

Nardole looked from the Doctor to Bill. “We have to get him into the TARDIS.”

Bill nodded, and brushed a thumb through the Doctor’s hair. His head turned slightly toward her and then his eyes mercifully opened, watery and exhausted, but still vaguely alert. 

“Bill.”

Bill smiled and set a hand on his shoulder. “Hey; I’m here. You’re gonna be alright.”

She looked at Nardole. Neither of them knew if she was lying or not. 

Nardole turned to Missy, who still hovered by the TARDIS doors.

“Help us.”

...

Bill sat with her head leaned on her hand, memorizing the rhythm of the Doctor’s slow breathing and noting the little twitches of his face as he slept. Beneath her eyes, she knew, lay bags and tear tracks she hadn’t dared show in front of the Doctor or anyone else. 

Every now and then the blanket would shift and reveal the bandage covering the Doctor’s injury, and Bill would be hit with flashbacks. Carrying him to his room was the simplest part. After that had come twenty minutes of wrestling with him to stay still, and trying to ignore his protests when they hurt him as they tried to heal him. And then there was the minute Nardole had to act as his hearts and lungs...

The worst of it, though, had been Missy. She had always there, lurking, offering help that Nardole ardently refused. Bill felt altogether sorry for her and immensely angry. 

The Doctor’s breathing pattern suddenly changed, and Bill raised her head up to watch him. Slowly, his eyes began moving beneath their lids, and then opened. As his brows furrowed in an unspoken question, Bill took his hand.

“Hey, it’s alright. You’re okay,” she assured, shifting to the edge of her seat to be close to him. “We’re in the TARDIS.”

He swallowed and looked down at himself, noticing that only bandages covered his chest.

“Nardole fixed you up. He’s full of surprises.” She smiled, but it didn’t reach her exhausted eyes. Instead, a tear fell from them.

The Doctor raised his free hand to her face and caught the tear on the pad of his thumb. Bill wiped her face in her sleeve and took in a deep breath, trying to be nonchalant.

“We were worried about you. You…” Bill broke off. She cleared her throat to continue. “We almost lost you.”

Her voice faded away, and she looked down. The Doctor’s hand lifted her chin back up. With a voice more tired than Bill felt, he said, “I’m not going anywhere.”

Bill smiled. This time, it reached her eyes. “Don’t do that to us again though, eh?”

“I promise.”

The door opened with a soft creak. “Hey hey! Look who’s finally awake.”

Nardole put a hand on Bill’s shoulder. “She wouldn’t let herself sleep until you woke up.” Nardole rolled his eyes playfully. “Humans.”

Bill lightly punched his arm in response. Nardole practically squeaked, earning a chuckle from the Doctor. A moment later, though, he closed his eyes again and groaned.

“Yeah, sorry about that,” Nardole explained. “It’s gonna be sore for a little while. You know, we had to restart your hearts at one point.”

His simple words hit the Doctor and Bill hard. He looked to her as she looked to the floor. 

Nardole cleared his throat and put on a falsely chipper expression. “Anyway, Miss Potts, I think it’s time you took a nap. I’ll watch over him. Make sure he doesn’t get into trouble. That’s basically my job descriptiom.”

Bill only faced the Doctor again when she reached the door. “Feel better soon, Doctor.”

The Doctor tried to push himself up, stopped by Nardole and weak muscles. “I’ll see you soon, Bill.”

They shared another smile before Bill left the room, closing the door behind her as she entered the hallway. A shadow in the distance caused her throat to close up.

“How is he?”

She passed right by Missy without looking at her. Then, she spun back around to find the woman handcuffed to a wooden chair. She looked smaller and less threatening than ever.

“He’s going to be fine.” She approached Missy with anger rising. “You know, he could have died. He did die. For a minute there, he wasn’t breathing. His hearts stopped. Nardole had to resuscitate him and I felt useless because my best mate was dying and I couldn’t do anything to help. And that was all because of you.”

Missy opened her mouth to speak, but no words came. Bill leaned toward her. “I have no idea who you are or why the Doctor still trusts you, but I don’t think I can do it anymore.”

“Bill,” Missy pulled on her handcuff, and Bill shrank away.

“Don’t,” she said. “Just leave me alone.”

Bill walked down the long corridors until she found an empty bedroom far away from both Time Lord and Time Lady.

…

The Doctor stood leaned heavily on the Console, a white shirt buttoned up to the pink mark on his chest, giving him a little bit of the privacy he’d missed in these past few days. Missy stood, still handcuffed, in front of him, as did Nardole and Bill. The Doctor took a shaky step toward the trio and adjusted his shirt cuff. Bill watched him with one eyebrow raised.

“I still think you’re mad,” she said.

“I’m fine.” He reached over to the railing and grabbed his jacket into his hand, barely hiding a grimace of pain. “I need to get out. Timelords aren’t meant to be in bed for long.”

Bill shrugged, unconvinced. “If you say so.”

She had to admit, a large part of her was glad he was back on his feet so quick, and now wearing that Doctorly coat with the colorful lining again. But every time a pain would hit him, she was reminded of that horrible night. The anxiety and the tears and the thought of never seeing him again had given her a great feeling of protectiveness over him.

She buttoned the rest of his shirt up to the top and dusted off his shoulders, then pulled him into a hug. “I’m really glad you’re alright, Doctor.”

“Me too,” Nardole said, approaching the Doctor from behind. The Doctor groaned.

“No, no really-”

Nardole put his arms around the Doctor, who patted him on the arm awkwardly. When they finally released him, he coolly adjusted his jacket. Bill put her hands in her pockets.

“So what are we gonna do with, er,” she nodded toward Missy. 

“Ah, yes, actually I thought about that,” the Doctor said. “Nardole, Bill; can you give us a moment?”

Their jaws dropped. 

Nardole said, “Doctor, you realize.”

“Yes,” the Doctor said with a hand up. “I know.”

“But seriously, Doctor,” Bill quipped.

The Doctor nodded. “I know. Just a moment. We’ll be fine.”

Nardole and Bill looked at each other, and hesitantly walked out of the TARDIS together. At the last moment, Bill called, “Shout if you need us!”

The Doctor fiddled with a few controls on the TARDIS, adjusting screen settings and whatnot to avoid meeting her gaze. It was no matter, for she was eyeing the floor like it was a da Vinci.

“I’m guessing you’re not going to bring me back,” Missy said finally. The Doctor furrowed his eyebrows.

“Why wouldn’t I? I told you I forgave you. Or was that in my head? Sorry, got a bit blurry for a minute there.”

Missy looked up at him. “You seriously forgave me? For what I did? I almost killed you, you prawn!”

“I didn’t die,” the Doctor said with a smirk. “See? I’m fine.”

“Your hearts stopped beating. Because of me. How can you possibly-?”

“Because before all else, you were my friend.” He started toward her. “I can never not forgive you.”

She stepped back, bewildered. “What are you doing?”

The Doctor didn’t reply, only came closer. When he was a foot away from her, he raised his arms and pulled her into a hug. Missy let out a breathy gasp. The Doctor closed his eyes and let her head rest against his shoulder as she started crying.

As soon as Nardole and Bill heard crying coming from the TARDIS, they threw open the doors. When they saw the Doctor embracing Missy as she weeped, their fear turned into sudden confusion. Bill shook her head.

“I will never understand that relationship.”

…

 

Bill sat writing her latest essay -- The Uniqueness of Planet Earth -- pretending not to notice the distracted Doctor sitting across the desk fiddling with everything except his lecture notes.

The Doctor sat tapping his pencil on the desk with about a thousand things on his mind, but only one answer.

“We run because the past can hurt us,” he said, staring at some distant point on the wall behind her. “Because we want to forget.” 

Bill looked up from her essay and set her pencil down. “Nah, you never forget. Not one person.”

The Doctor tilted his head, debating. “Maybe that’s why I keep running.”

Bill leaned back, crossing her arms. “Mmm.”

“Okay,” The Doctor said, leaning forward. “Do you have a better idea?”

Bill pondered it for a moment. “You run because because if you don’t run, then people will either be with you or against you. And you don’t want people to pick sides and all that; you’re just a bloke trying to travel, not a politician. So you run. Then they can have a choice. They can keep doing whatever bad thing they’d doing, or they can change.”

The Doctor leaned his chin on folded hands. “Hm.”

Bill quirked an eyebrow. “What?”

The Doctor shook his head, blinking out of his thoughts. “I need to pull back on my tutoring. Pretty soon you won’t need me anymore.”

Bill pushed away all of the thoughts fixating on that last sentence. Instead, she put her hands on the table and smiled. “You know what? Are your hearts all better?”

The Doctor nodded. “Pretty much.”

“Then come on. Me and you; chips break.”

Bill stood. The Doctor raised a brow. “Chips break?”

Bill held out her hand. “Yep. My mate Alex is serving tonight, and we could both use some comfort food.”

The Doctor smiled. “Sounds good to me.”

Bill led the way out of the office and down the beautiful wooden staircase, letting herself forget about running and good and evil and aliens. Letting herself be a young woman having dinner with her best friend. Life had never been better.


End file.
